Human enterovirus 71 (EV71) is a major causative agent of hand, foot, and, mouth disease, accounting for more than 65% of recent outbreaks. Following enteroviral infection, the host responses are crucial indicators for the development of a diagnosis regarding the clinical severity of EV71 infections. In this study, we implemented NanoString nCounter technology to characterize the responses of serum microRNA (miRNA) profiles to various EV71 infection diseases. Upon EV71 infection, 44 miRNAs were observed in patients with EV71 infections, with at least a 2-fold elevation and 133 miRNAs with a 2-fold reduction compared with the same miRNAs in healthy controls. Further detailed work with miR876-5p, a 9.5-fold change of upregulated miR-876-5p expression was observed in cases with severe EV71 symptoms, revealed that in vitro and in vivo knockdown of miR876-5p reduced viral RNA in cultured cells, and attenuated the severity of symptoms in EV71-infected mice. Altogether, we demonstrated that the elevated expression of circulating miR876-5p is a specific response to severe EV71 infections.